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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/ksw2">Debian Med / ksw2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ksw2/-/commit/80e41cf545274c5b371d3ff41c07c7d35326fbb5">80e41cf5</a></strong>
<div>
<span>by Etienne Mollier</span>
<i>at 2020-07-11T12:43:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">check and use operating system libgaba
build dependency to an hypothetical libgaba-dev is not ready yet, but
could be in a the future.
</pre>
</li>
</ul>
<h4>1 changed file:</h4>
<ul>
<li class="file-stats">
<a href="#6d5507768ac8975f221ead23baef90cb894ce802">
debian/patches/autoconf.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="6d5507768ac8975f221ead23baef90cb894ce802">
<a href="https://salsa.debian.org/med-team/ksw2/-/commit/80e41cf545274c5b371d3ff41c07c7d35326fbb5#6d5507768ac8975f221ead23baef90cb894ce802"><strong>debian/patches/autoconf.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,7 +26,7 @@ Description: Provide automake build system to get proper library packaging</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ksw2/configure.ac</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="p">@@ -0,0 +1,6<span class="idiff left right">6</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="p">@@ -0,0 +1,6<span class="idiff left right">7</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# -*- Autoconf -*-</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Process this file with autoconf to produce a configure script.</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -81,6 +81,7 @@ Description: Provide automake build system to get proper library packaging</td>
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<td class="diff-line-num old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_HEADER_STDC</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CHECK_HEADERS([stdlib.h])</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CHECK_HEADERS([parasail.h],[AC_DEFINE([HAVE_PARASAIL], [1], [Use parasail])])</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CHECK_HEADERS([gaba.h],[AC_DEFINE([HAVE_GABA], [1], [Use libgaba])])</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_PROG_MAKE_SET</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -171,7 +172,12 @@ Description: Provide automake build system to get proper library packaging</td>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_gg2_sse.o: ksw2.h</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ksw2.orig/cli.c</span></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ksw2/cli.c</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="p">@@ -7,11 +7,11 @@</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> KSEQ_INIT(gzFile, gzread)</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> </span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> #ifdef HAVE_GABA</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include "gaba.h"</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <gaba.h></span></span>
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175
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="diff"> #endif</span>
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176
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="diff"> </span>
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177
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="diff"> #ifdef HAVE_PARASAIL</span>
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